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We're interested in enhancing the ML/MM method by including intermolecular interactions between the ML and MM regions of the system. There is some discussion on the slack channel for this about which …
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We need a new CLI analysis tool (which can also be run via the Python API) to analyze simulations set up via the perses CLI.
It should provide three major outputs:
1. **Optimal predictions:** The …
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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Learn something every day...
Per the VIM and GUM, the term 'confidence interval' (See VIM, definition 2.36 [coverage interval], Note 2; or GUM 6.2.2) should not be used. This would involve a lot of…
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Hi flamel team,
Thank you for your work on flamel, it's a great tool. We are trying to use for our system, and we are getting the following issue:
_Traceback (most recent call last):
File "/h…
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Dear Yanze,
I hope this message finds you well. I have a quick question regarding the mod_system_no_mol.top file that you provided. As I understand, this file was generated using AMBERTOOL.
My i…
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It could be useful to support simulations with explicit space group symmetry, along the lines of http://pubs.acs.org/doi/abs/10.1021/ct100506d. I think this could be done with just another type of vi…
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This is from https://github.com/openmm/openmm-cookbook/issues/28
If you run the [Alchemical Free energy tutorial](https://openmm.github.io/openmm-cookbook/latest/notebooks/tutorials/Alchemical_free…
sef43 updated
5 months ago
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Dear Professor Gallicchio,
While using AToM, I realized that there are two versions of control files in terms of the parameters including LAMBDA1, LAMBDA2, ALPHA, U0, UMAX and UBCORE.
In RBFE …
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I think it might be worthwhile to add an enhancement to the [createMixedSystem](https://github.com/openmm/openmm-ml/blob/4f0546678eeb9b2703d28d3fce7f678802640701/openmmml/mlpotential.py#L177) function…